The Northern Territory child protection system is under enormous strain with case workers in some regional centres managing three times more children than they should be, figures show.

Data seen by the ABC revealed that as of June 30, Katherine's 14 case workers had more than 90 children each assigned to them.

Chief executive of the Department of Territory Families, Ken Davies, said an "ideal scenario" would see each case worker managing between 25 and 30 children.

"It is still very high [in Katherine], and we acknowledge that," Mr Davies said.

"In fact if you look at the data, it's really in keeping with the Arnhem office, which is also very high.

"Both of those places are a concern for us and that's why we have the recruiting programs that we do in place," Mr Davies said.

The figures showed that at the end of June, the Arnhem region, which covers Yirrkala, Nhulunbuy and Maningrida, had eight child protection officers with 49 cases each.

Mr Davies said a failure of the Department to "administratively close" cases, as well as problems recruiting staff had contributed to the high figures, but that those excuses did not explain away the data.

Across the Northern Territory's eight regions, just one office, Casuarina in Darwin, was meeting the ideal number of cases per child protection officer.

Aboriginal child placement principle 'not being followed'

The Department's annual report revealed case workers were not routinely adhering to the principle of placing Aboriginal children in kinship care, where they are cared for by relatives or close family friends.

In the past year there was a 3.7 per cent drop in the number of Aboriginal children being placed with Aboriginal carers.

Last financial year just under 32 per cent of children were placed with Aboriginal carers.